We present the Hilbert-Huang transform (HHT) analysis on the quasi-periodic modulation of SMC X-1. SMC X-1, consisting of a neutron star and a massive companion, exhibits superorbital modulation with a period varying between ~40 d and ~65 d. We applied the HHT on the light curve observed by the All-Sky Monitor onboard Rossi X-ray Timing Explorer (RXTE) to obtain the instantaneous frequency of the superorbital modulation of SMC X-1. The resultant Hilbert spectrum is consistent with the dynamic power spectrum while it shows more detailed information in both the time and frequency domains. According to the instantaneous frequency, we found a correlation between the superorbital period and the modulation amplitude. Combining the spectral observation made by the Proportional Counter Array onboard RXTE and the superorbital phase derived in the HHT, we performed a superorbital phase-resolved spectral analysis of SMC X-1. An analysis of the spectral parameters versus the orbital phase for different superorbital states revealed that the diversity of $n_H$ has an orbital dependence. Furthermore, we obtained the variation in the eclipse profiles by folding the All Sky Monitor light curve with orbital period for different superorbital states. A dip feature, similar to the pre-eclipse dip of Her X-1, can be observed only in the superorbital ascending and descending states, while the width is anti-correlated with the X-ray flux.